Pokemon Apex Soul
by NumberofWattage
Summary: A line exists to divide Man and Pokemon. The deadly Team Apex arrive in the Johto Region to disrupt that line and throw the Pokemon World into chaos, but they timed their scheme just as the destined hero of the Hoenn region was set to move away. Destiny now shifted, Brendan will instead remain to conquer Johto and uncover the horror of The Apex Machine


**Pokemon Apex Soul**

By NumberofWattage

Disclaimer: The following is an alternate universe fan work. Pokemon Silver, Soul Silver, Ruby and Omega Ruby are owned by Nintendo, Game Freak, Creatures and Satoshi Tajiri. Please support the official release. Also, I think Team Four Star or somebody gets credit for the disclaimer format.

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Chap. 1

 _"-In local news, Norman, esteemed Gym Leader of Goldenrod City, announced this morning that he would be stepping down later this week to take up the post in Hoenn's Petalburg City. Citing personal reasons for his departure, League officials have indicated that Norman will be succeeded by his young protégé Ace Gym Trainer Whitney in-_ *Click*"

Brendan groaned sleepily, hand slipping off his old Hoothoot shaped alarm clock. He reflected that he'd hate to be at the Goldenrod Gym today, it was going to be a circus after that announcement. Luckily, he worked as a Gym Trainer closer to home, at the Olivine Gym. Vertebrae popped in his sore back from a late packing session the night before with his cruel taskmaster of a mother as the Youngster Gym Trainer rolled out of bed-

" _Shhhuntrew_!"

-Directly on top of his Sandshrew, who yelped as the two tangled and thrashed in the sheets, boy and Pokemon both trying to extract themselves from the other.

The ball of limbs and fury tumbles across the floor and began toppling moving boxes full of books, clothing and toys in their wake until Sandshrew finally gnawed a hole in the bedding and embraced freedom.

A scratched and bruised trainer finally untangled himself as well, finding the Pokemon furiously licking at the fine pale fur of it's underbelly atop the stripped down bed. Brendan sighed. He and Sandshrew weren't particularly attached to each other, but she wasn't actually his, either. She was issued to him from the Olivine Gym rotation when he took a position among the Trainer gauntlet for Leader Jasmine. He liked her fine, but never thought of her as an actual partner and she was a obedient if bit stand-offish, though they were rather decent as a battle team.

Today would be their last day together.

He patted her head briefly and the Mouse Pokemon paused her grooming and perked up a bit.

"Sorry, girl." he murmured "You, at least, get to stay here. I get shipped to Hoenn in a crate."

His mom, for reasons best known to herself and whatever force drove her to torment her progeny so, had gotten it into her head that it was every young man's dream to traverse two regions in a the back of a moving truck amongst the cargo. They were leaving in less than a week and he had to tie up everything with work and packing before then.

The Pokemon seemed to respond to his mood. She chirped and nuzzled apologetically at a few of the scratches she had given him.

"That's fine." he stretched and meandered a bit as he dressed and cleaned up. Sandshrew bounded downstairs ahead of him and chirped for breakfast. Mom was at the Moomoo Farm where she worked long before he woke up in the morning and Dad was usually away from home in Goldenrod City, so Brendan just scrounged from the almost empty perishables he had been told to finish off and divided some of them with the little Ground type.

Glancing at the microwave clock, he noted with some surprise that it was only 7:04. He usually snoozed his alarm at least twice in the morning. His apprehension about moving must be affecting him more than he thought.

"Huh. Well, let's hurry it up, we can surprise the boss if we're early for once."

 _"Shrru."_ Sandshrew squeaked blandly, mouth full of a celery stalk.

Yes, he was apprehensive. Things were changing for his family.

He didn't particularly want to move to Hoenn. That was for his workaholic father. It was pointless to even move, in Brendan's opinion, as either way he was going to always be hanging around a Gym for weeks on end doing the same thing he did now and still several towns away from his family. Dad was even going ahead of them to open the Petalburg Gym and probably wouldn't even see them in Littleroot Town for a while.

Brendan just wished they could stay in Johto.

When they finished and he recalled the Pokemon to her Pokeball, Brendan took his white knit cap from it's hook by the front door and pulled it over his head. He breathed the strong sea breeze outside. He jumped the three steps of their front stoop then turned and walked from his house near the Port towards the north end of town, to his final day at the Gym.

* * *

Olivine city was a large but compact port city, partially spread over a sheer cliff face on the southern coast with the towering Glitter Lighthouse far to the southeast guiding ships from as far away as Kalos and Unova to the Olivine Port. To the west, the cliffs gave way to the beach and the Port to the shopping district, with restaurants overlooking the ocean. Most residences were situated in the center and north.

Furthest to the north, and the largest building aside from the signature Lighthouse, was the sloping gray dome fixture of the Olivine City Gym.

Leader Jasmine hefted a large bag into her rusty old Graveler drawn cart. The Rock type Gym Leader was a slim teenager of deceptive strength and a sweet temperament. Her patience, however, was running thin.

She tiredly perched herself atop her Pokemon, looking about for her last staff member. He was always running late, that Brendan. The young woman shook dust from her long brown hair and checked her nails as she puffed an exasperated breath.

They should have already been past Moomoo Farm by now, she just hoped the boy hadn't decided to blow off his last day of work.

Brendan was such a great worker, despite his usual tardiness. The front trainer of the roster, he and Sandshrew made a great first impression for the Gym with their wit and a decent challenge for young trainers and though he had no Pokemon of his own, he took care of the Gym Pokemon with enthusiasm. She could always count on him.

 _"Hrrrr"_ Graveler grunted to catch her attention and she looked his direction the see a distinctive white cap bobbing through the sparse morning crowd.

"Well, somebody's late." she said dryly as he strolled up.

Brendan blinked "Late? I'm not late, it's only 7:50"

"It's 8:30" she pushed her watch at his face. He went a bit cross eyed trying to see it.

"Uh, boss? That says 8:30 PM. It's morning." he pointed out.

Jasmine stared at the Twelve year old and then quickly started fiddling with the wristwatch. It was... "All scrambled!" she wailed "I cant change it!"

"I told you that those Magnemite you got would mess with your electronics." Brendan drawled.

"Oh, I'm sooo sorry, Brendan!" she leapt from her perch and took up his hands in sorrow. "I accused you-"

"What's the cart for?" He changed the subject before his Leader could get too upset. Poor Jasmine was almost always proven wrong the second she tried to act the assertive boss, it wrecked havoc on her self-esteem.

"Oh!" She brightened up at an alarming speed "I almost forgot, we won't be late after all! We're not opening the Gym, instead you and I are going to Route 38 today. Professor Elm is bringing some equipment from his lab to study the Farfetch'd migration and we're going to help. I'm bringing some of my dad's old nature blinds along. The Professor is also going to give us a young Flaaffy to take over the Lighthouse. Our old Voltorb deserves to retire."

"Cool!" Brendan enthused "Can I meet the Professor?"

She gave a small laugh "Of course. Elm is great with young trainers. Just keep quiet around the Farfetch'd and it should be fine."

The young trainer grinned.

* * *

Brendan didn't stop grinning as his Leader's Graveler carted them across the picturesque countryside inland of Olivine. He was going to meet Elm, the foremost Pokemon Professor of the region! He was going to see the man at work in the field! This was easily the best he'd felt since Dad told him and Mom the "good news".

Jasmine was also smiling faintly at his enthusiasm. His tension was visibly eased from the last time she'd seen him.

"Ah, excuse me?"

Brendan and Jasmine started and looked to the grassy left of Route 38. A young woman was calling to them from the fence of the Moomoo Farm. She was a pretty girl with an elaborate hairstyle and an elegant deep red kimono. As their cart drew near, the duo could see that the expensive looking floral obi about her waist was snagged on a wire jutting from the fence.

"Yes, hello you two." she called softly "I- I'm afraid I need assistance. You see, I was trying to hide among the Miltank, such lovely Pokemon, and my obi was caught. I can't seem to reach it without causing a bad tear, and I love this obi so!"

"Why is she dressed like that at a farm?" Jasmine whispered to Brendan.

Shrugging and not bothering to mention that she was wearing a white dress to work in the field, he hopped from his seat and jogged over to the Kimono Girl.

"Thank you very much, young man." she said politely, though he could tell that she wasn't actually much his senior, probably close to Jasmine's age. "Just lift the bow a little, I believe the wire went through the knot." Up close he could tell that she was bent at an uncomfortable angle from being hung up a bit lower than she could stand and the sharp wire was indeed hooked through the knot from the top.

"I'm Brendan, by the way." he lifted the wire and frowned as it tugged at the fine silk brocade.

"A pleasure to meet you, Brendan." she smiled over her shoulder at him.

She finally came free and gracefully straightened and turned to regard him. Still smiling, she gave him a short formal bow and he quickly bowed back. "Thank you, Brendan."

"Why were you trying to hide with the Miltank?" he asked curiously. Jasmine also approached them.

The Kimono Girl inclined her head "Oh, well there was a group of very shady characters along the path not moments before your cart came into view." she replied.

"Shady characters?" Jasmine murmured, concerned.

"Yes, quite suspicious. They wore strange purple uniforms and masks as white as death itself which distorted their voices and I felt dread as a cold blade in my heart. They were making haste toward Route 38 and moved oddly, like predatory Pokemon stalking something."

They were heading toward Professor Elm, as well.

Brendan suddenly got a bad feeling in the pit of his stomach.

"Oh my." Jasmine whispered in horror. She had realized it as well.

The Gym Leader's demeanor turned authoritative "Let's go, Brendan." she said rushing back to Graveler.

"Excuse us." Brendan quickly bowed again and ran after her.

"Hurry!"

Brendan dashed past the cart. "I'm cutting through the woods to the Professor!" He yelled to his Leader.

"Go, I'll go by the Route!" Graveler lurched into action northward.

The young trainer rushed to the steep hill, sending Sandshrew from her ball in a flash of light.

"Rock Climb!" he ordered the Mouse Pokemon, gripping the grooves of her hard shell. "Hurry."

The Pokemon flung herself and the Trainer up the rocky wall with incredible strength. The two then dashed into a narrow path at the tree line.

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 **NoW: Okay, ending things there for now. I haven't been writing for about five years, I forgot that it was a bit of a challenge. Anyway, we're following the games timeline here, so this takes place in the Johto region concurrent to the Gen 1 Kanto games and the Gen 3 Hoenn games and three years before the Gen 2 Johto games. The Player character of Hoenn (Male option Brendan in this case) is apparently from Olivine, according to the wiki, so I'm rolling with that.**

 **Next chapter should be a bit predictable, we meet our villainous Team Apex, find out a bit of their gimmick, our hero gets a Starter Pokemon from Elm and explains to his clearly deranged mother that he's doing a Johto fanfic, damn it.**


End file.
